Approximate Reachability for Dead Code Elimination in Esterel*

Esterel is an imperative synchronous programming language for the design of reactive systems. Esterel* extends Esterel with a non-instantaneous jump instruction (compatible with concurrency, preemption, etc.) so as to enable powerful source-to-source program transformations, amenable to formal verification. In this work, we propose an approximate reachability algorithm for Esterel* and use its output to remove dead code. We prove the correctness of our techniques

Dextran sulfate enhances the level of an oxidative DNA damage biomarker, 8-oxo-7,8-dihydro-2'-deoxyguanosine, in rat colonic mucosa.

International audienceDextran sodium sulfate (DSS) given in drinking water can induce colonic inflammation and produce colorectal tumors in rodents, although it is not directly genotoxic. The hypothesis that DSS can produce free radicals and induce oxidative DNA damage in colonic mucosa has been tested. In rats fed for 2 days with water containing 3% and 6% DSS, colonic inflammation manifestations were recorded and 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxodGuo), a major biomarker of oxidative DNA damage, was assayed in colonic mucosa. As compared with control rats given pure water, inflammatory manifestations were seen in rats given DSS. At the same time, 8-oxodGuo levels in colonic mucosa were doubled (P < 0.001). These results suggest that formation of oxidative DNA damage in colonic mucosa depends on inflammation and maybe on the production of reactive oxygen species. This study shows that DSS can induce oxidative DNA damage within only 2 days, which could explain in part its carcinogenic properties

Rewriting Logic Semantics of a Plan Execution Language

The Plan Execution Interchange Language (PLEXIL) is a synchronous language developed by NASA to support autonomous spacecraft operations. In this paper, we propose a rewriting logic semantics of PLEXIL in Maude, a high-performance logical engine. The rewriting logic semantics is by itself a formal interpreter of the language and can be used as a semantic benchmark for the implementation of PLEXIL executives. The implementation in Maude has the additional benefit of making available to PLEXIL designers and developers all the formal analysis and verification tools provided by Maude. The formalization of the PLEXIL semantics in rewriting logic poses an interesting challenge due to the synchronous nature of the language and the prioritized rules defining its semantics. To overcome this difficulty, we propose a general procedure for simulating synchronous set relations in rewriting logic that is sound and, for deterministic relations, complete. We also report on two issues at the design level of the original PLEXIL semantics that were identified with the help of the executable specification in Maude

Theory of Cylindrical Tubules and Helical Ribbons of Chiral Lipid Membranes

We present a general theory for the equilibrium structure of cylindrical tubules and helical ribbons of chiral lipid membranes. This theory is based on a continuum elastic free energy that permits variations in the direction of molecular tilt and in the curvature of the membrane. The theory shows that the formation of tubules and helical ribbons is driven by the chirality of the membrane. Tubules have a first-order transition from a uniform state to a helically modulated state, with periodic stripes in the tilt direction and ripples in the curvature. Helical ribbons can be stable structures, or they can be unstable intermediate states in the formation of tubules.Comment: 43 pages, including 12 postscript figures, uses REVTeX 3.0 and epsf.st

Non-monotonic variation with salt concentration of the second virial coefficient in protein solutions

The osmotic virial coefficient $B_2$ of globular protein solutions is calculated as a function of added salt concentration at fixed pH by computer simulations of the ``primitive model''. The salt and counter-ions as well as a discrete charge pattern on the protein surface are explicitly incorporated. For parameters roughly corresponding to lysozyme, we find that $B_2$ first decreases with added salt concentration up to a threshold concentration, then increases to a maximum, and then decreases again upon further raising the ionic strength. Our studies demonstrate that the existence of a discrete charge pattern on the protein surface profoundly influences the effective interactions and that non-linear Poisson Boltzmann and Derjaguin-Landau-Verwey-Overbeek (DLVO) theory fail for large ionic strength. The observed non-monotonicity of $B_2$ is compared to experiments. Implications for protein crystallization are discussed.Comment: 43 pages, including 17 figure

SCCharts: Sequentially Constructive Statecharts for Safety-Critical Applications

We present a new visual language, SCCharts, designed for specifying safety-critical reactive systems. SCCharts uses a new statechart notation and provides deterministic concurrency based on a synchronous model of computation (MoC), without restrictions common to previous synchronous MoCs. Specifically, we lift earlier limitations on sequential accesses to shared variables, by leveraging the sequentially constructive MoC. The key features of SCCharts are defined by a very small set of elements, the Core SCCharts, consisting of state machines plus fork/join concurrency. Conversely, Extended SCCharts contain a rich set of advanced features, such as different abort types, signals, history transitions, etc., all of which can be reduced via model-to-model transformations into Core SCCharts. This approach enables a simple yet efficient compilation strategy and aids verification and certification

Equation of state and phonon frequency calculations of diamond at high pressures

The pressure-volume relationship and the zone-center optical phonon frequency of cubic diamond at pressures up to 600 GPa have been calculated based on Density Functional Theory within the Local Density Approximation and the Generalized Gradient Approximation. Three different approaches, viz. a pseudopotential method applied in the basis of plane waves, an all-electron method relying on Augmented Plane Waves plus Local Orbitals, and an intermediate approach implemented in the basis of Projector Augmented Waves have been used. All these methods and approximations yield consistent results for the pressure derivative of the bulk modulus and the volume dependence of the mode Grueneisen parameter of diamond. The results are at variance with recent precise measurements up to 140 GPa. Possible implications for the experimental pressure determination based on the ruby luminescence method are discussed.Comment: 10 pages, 6 figure

Phase equilibria and glass transition in colloidal systems with short-ranged attractive interactions. Application to protein crystallization

We have studied a model of a complex fluid consisting of particles interacting through a hard core and a short range attractive potential of both Yukawa and square-well form. Using a hybrid method, including a self-consistent and quite accurate approximation for the liquid integral equation in the case of the Yukawa fluid, perturbation theory to evaluate the crystal free energies, and mode-coupling theory of the glass transition, we determine both the equilibrium phase diagram of the system and the lines of equilibrium between the supercooled fluid and the glass phases. For these potentials, we study the phase diagrams for different values of the potential range, the ratio of the range of the interaction to the diameter of the repulsive core being the main control parameter. Our arguments are relevant to a variety of systems, from dense colloidal systems with depletion forces, through particle gels, nano-particle aggregation, and globular protein crystallization.Comment: 20 pages, 10 figure